Accurate bookkeeping is the backbone of every successful business. For Ontario businesses, choosing the right bookkeeping software is critical to staying compliant with CRA requirements, managing HST (13%), and preparing reliable financial reports.

In this guide, we review the best bookkeeping software for Ontario businesses in 2025, with a primary focus on QuickBooks Online (QBO)—the most widely used and CRA-friendly accounting software in Canada.

Why Bookkeeping Software Matters for Ontario Businesses

Using proper bookkeeping software helps Ontario business owners:

• Stay compliant with CRA and Ontario tax rules
• Track HST accurately
• Prepare for corporate and personal tax filings
• Reduce audit risk
• Save time and avoid manual errors

Whether you’re a sole proprietor, incorporated business, freelancer, or contractor in Ontario, the right software can make a significant difference.

Top Bookkeeping Software for Ontario Businesses (2025)

1. QuickBooks Online (QBO) – Best Overall Choice ⭐⭐⭐⭐⭐

Best for:

Ontario small businesses, corporations, freelancers, and independent contractors

Why QuickBooks Online is #1 in Ontario:

• Fully CRA-compliant
• Supports HST (Ontario 13%)
• Seamless bank and credit card integrations
• Strong payroll and expense tracking
• Compatible with most Ontario CPA firms
• Cloud-based and accessible anywhere

Key Features:

• Automated bank feeds
• HST tracking and reporting
• Invoicing and receipt capture
• Payroll integration
• Financial statements (P&L, Balance Sheet)

📌 CPA Insight:

QuickBooks Online is the preferred software used by most Ontario CPAs, making year-end tax filing faster and more cost-effective.

2. Wave Accounting – Budget-Friendly Option

Best for:

Ontario sole proprietors and very small businesses

Pros:

• Free basic bookkeeping
• Simple invoicing
• Easy to use

Cons:

• Limited HST reporting
• Weak scalability
• Not ideal for incorporated businesses

3. Xero – Strong Alternative for Growing Businesses

Best for:

Ontario businesses with complex inventory or multi-currency needs

Pros:

• Clean interface
• Strong reporting tools

Cons:

• Less commonly used by Ontario CPAs
• HST setup can be less intuitive than QBO

Why Ontario Businesses Prefer QuickBooks Online

QuickBooks Online is specifically well-suited for Ontario businesses because it:

• Handles Ontario HST rules accurately
• Integrates with CRA-compliant payroll systems
• Supports corporate, sole proprietor, and partnership reporting
• Allows seamless collaboration with your CPA
• Scales as your business grows

From startups to established corporations, QBO remains the gold standard in Ontario.

Bookkeeping Software by Business Type (Ontario)

Sole Proprietors & Freelancers

✅ QuickBooks Online Simple Start

✅ Wave (basic only)

Incorporated Businesses

✅ QuickBooks Online Plus or Advanced

❌ Wave (not recommended)

Contractors & Consultants

✅ QuickBooks Online Essentials

✅ Xero (case-specific)

Common Bookkeeping Mistakes Ontario Businesses Make

• Using spreadsheets instead of accounting software
• Not tracking HST correctly
• Mixing personal and business expenses
• Poor bank reconciliations
• Not reviewing books monthly

Using QuickBooks Online with CPA oversight eliminates most of these risks.

Frequently Asked Questions (FAQs)

What is the best bookkeeping software for Ontario businesses?

QuickBooks Online is the best bookkeeping software for most Ontario businesses due to its CRA compliance, HST support, and CPA integration.

Is QuickBooks Online CRA-approved?

Yes. QuickBooks Online is widely accepted and used by CRA-registered tax professionals across Ontario.

Can QuickBooks Online handle Ontario HST?

Yes. QBO supports Ontario’s 13% HST and allows accurate tracking, reporting, and filing preparation.

Is bookkeeping software mandatory in Ontario?

While not legally required, using bookkeeping software is strongly recommended to meet CRA record-keeping requirements.

Can a CPA access my QuickBooks Online file?

Yes. One of QBO’s biggest advantages is real-time collaboration with your Ontario CPA.